{"id":15027720,"url":"https://github.com/jokergoo/complexheatmap","last_synced_at":"2025-05-14T12:12:16.255Z","repository":{"id":26563716,"uuid":"30017750","full_name":"jokergoo/ComplexHeatmap","owner":"jokergoo","description":"Make Complex Heatmaps ","archived":false,"fork":false,"pushed_at":"2025-04-01T16:51:46.000Z","size":16003,"stargazers_count":1357,"open_issues_count":219,"forks_count":234,"subscribers_count":34,"default_branch":"master","last_synced_at":"2025-04-04T00:03:17.305Z","etag":null,"topics":["clustering","complex-heatmaps","heatmap"],"latest_commit_sha":null,"homepage":"https://jokergoo.github.io/ComplexHeatmap-reference/book/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jokergoo.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-01-29T11:45:58.000Z","updated_at":"2025-04-03T03:12:17.000Z","dependencies_parsed_at":"2022-07-14T03:40:30.234Z","dependency_job_id":"68209ab3-0fbc-4c58-a9ea-d0ba85b1db4b","html_url":"https://github.com/jokergoo/ComplexHeatmap","commit_stats":{"total_commits":1413,"total_committers":28,"mean_commits":"50.464285714285715","dds":0.3113941967445152,"last_synced_commit":"3398d2157df844f4acd5202148dd87a54ca7cb62"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jokergoo%2FComplexHeatmap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jokergoo%2FComplexHeatmap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jokergoo%2FComplexHeatmap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jokergoo%2FComplexHeatmap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jokergoo","download_url":"https://codeload.github.com/jokergoo/ComplexHeatmap/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247097984,"owners_count":20883128,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["clustering","complex-heatmaps","heatmap"],"created_at":"2024-09-24T20:06:56.691Z","updated_at":"2025-04-04T00:03:35.018Z","avatar_url":"https://github.com/jokergoo.png","language":"R","readme":"# Make Complex Heatmaps \u003ca href=\"https://jokergoo.github.io/ComplexHeatmap-reference/book/\"\u003e\u003cimg src=\"https://jokergoo.github.io/ComplexHeatmap-reference/book/complexheatmap-cover.jpg\" width=240 align=\"right\" style=\"border:2px solid black;\" \u003e\u003c/a\u003e\n\n[![R-CMD-check](https://github.com/jokergoo/ComplexHeatmap/workflows/R-CMD-check/badge.svg)](https://github.com/jokergoo/ComplexHeatmap/actions)\n[![codecov](https://img.shields.io/codecov/c/github/jokergoo/ComplexHeatmap.svg)](https://codecov.io/github/jokergoo/ComplexHeatmap) \n[![bioc](http://www.bioconductor.org/shields/downloads/devel/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) \n[![bioc](http://www.bioconductor.org/shields/years-in-bioc/ComplexHeatmap.svg)](http://bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html)\n\n\u003cimg src=\"http://jokergoo.github.io/complexheatmap_logo.svg\" width=\"550\"\u003e\n\n\nComplex heatmaps are efficient to visualize associations between different\nsources of data sets and reveal potential patterns. Here the\n**ComplexHeatmap** package provides a highly flexible way to arrange multiple\nheatmaps and supports various annotation graphics.\n\nThe [**InteractiveComplexHeatmap**](https://github.com/jokergoo/InteractiveComplexHeatmap) package can directly export static complex heatmaps into an interactive Shiny app. Have a try!\n\n## Citation\n\nZuguang Gu, et al., [Complex heatmaps reveal patterns and correlations in multidimensional genomic data](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), Bioinformatics, 2016.\n\nZuguang Gu. [Complex Heatmap Visualization](https://doi.org/10.1002/imt2.43), iMeta, 2022. \n\n\n## Install\n\n`ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can install it by:\n\n```r\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"ComplexHeatmap\")\n```\n\nIf you want the latest version, install it directly from GitHub:\n\n```r\nlibrary(devtools)\ninstall_github(\"jokergoo/ComplexHeatmap\")\n```\n\n## Usage\n\nMake a single heatmap:\n\n```r\nHeatmap(mat, ...)\n```\n\nA single Heatmap with column annotations:\n\n```r\nha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...)\nHeatmap(mat, ..., top_annotation = ha)\n```\n\nMake a list of heatmaps:\n\n```r\nHeatmap(mat1, ...) + Heatmap(mat2, ...)\n```\n\nMake a list of heatmaps and row annotations:\n\n```r\nha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = \"row\")\nHeatmap(mat1, ...) + Heatmap(mat2, ...) + ha\n```\n\n## Documentation\n\nThe full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/ and the website is at https://jokergoo.github.io/ComplexHeatmap.\n\n## Blog posts\n\nThere are following blog posts focusing on specific topics:\n\n- [Make 3D heatmap](https://jokergoo.github.io/2021/03/24/3d-heatmap/)\n- [Translate from pheatmap to ComplexHeatmap](https://jokergoo.github.io/2020/05/06/translate-from-pheatmap-to-complexheatmap/)\n- [Set cell width/height in the heatmap](https://jokergoo.github.io/2020/05/11/set-cell-width/height-in-the-heatmap/)\n- [Interactive ComplexHeatmap](https://jokergoo.github.io/2020/05/15/interactive-complexheatmap/)\n- [Word cloud as heatmap annotation](https://jokergoo.github.io/2020/05/31/word-cloud-as-heatmap-annotation/)\n- [Which heatmap function is faster?](https://jokergoo.github.io/2020/06/19/which-heatmap-function-is-faster/)\n- [Rasterization in ComplexHeatmap](https://jokergoo.github.io/2020/06/30/rasterization-in-complexheatmap/)\n- [Block annotation over several slices](https://jokergoo.github.io/2020/07/06/block-annotation-over-several-slices/)\n- [Integrate ComplexHeatmap with cowplot package](https://jokergoo.github.io/2020/07/14/integrate-complexheatmap-with-cowplot-package/)\n\n\n## Examples\n\n### Visualize Methylation Profile with Complex Annotations\n\n![complexheatmap_example4](https://user-images.githubusercontent.com/449218/47718635-2ec22980-dc49-11e8-9f01-37becb19e0d5.png)\n\n### Correlations between methylation, expression and other genomic features\n\n![complexheatmap_example3](https://user-images.githubusercontent.com/449218/47718636-2ec22980-dc49-11e8-8db0-1659c27dcf40.png)\n\n### Visualize Cell Heterogeneity from Single Cell RNASeq\n\n![complexheatmap_example2](https://user-images.githubusercontent.com/449218/47718637-2ec22980-dc49-11e8-925e-955c16cfa982.png)\n\n### Making Enhanced OncoPrint\n\n![complexheatmap_example1](https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png)\n\n### UpSet plot\n\n\u003cimg src=\"https://user-images.githubusercontent.com/449218/102615477-48c76a80-4136-11eb-98d9-3c528844fbe8.png\" width=500 /\u003e\n\n### 3D heatmap\n\n![image](https://user-images.githubusercontent.com/449218/112284448-8c77c600-8c89-11eb-8d38-c5538900df20.png)\n\n\n\n## License\n\nMIT @ Zuguang Gu\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjokergoo%2Fcomplexheatmap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjokergoo%2Fcomplexheatmap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjokergoo%2Fcomplexheatmap/lists"}